Genomics and breeding of the fig tree, an ancient crop with promising perspectives

The availability of the genome sequence is a key prerequisite to apply modern breeding procedures to crops, and it is increasingly important to obtain the genomic variation data between the two haplotypes, representing a pivotal resource to study allele-specific expression. The fig tree (Ficus carica L.) has a great potential for commercial expansion thanks to its esteemed nutritional and nutraceutical characteristics, combined with its ability to adapt well to difficult environmental conditions. In this work, the fig genome represented the starting point to identifying intergenic and intragenic structural variations to better understand their functional impact. 540 syntenic regions were detected, corresponding to 95% of the fig genome. 2,700,243 single nucleotide polymorphisms (SNPs), 1,488,669 insertions/deletions (INDELs) and 8,360 structural variations (SVs) were identified between the syntenic regions. Overall, the intragenomic diversity was estimated at around 0.4%. 22,120 gene pairs were considered reliable allelic genes. Of these, 15,927 gene pairs showed genetic mutations, including presumed high impact mutations that were identified on 5,997 gene pairs. Specifically, a total of 230,612 mutations were identified, divided into 121,028 SNPs (52.48%) and 109,584 INDELs (47.52%). Most of these mutations were identified within the intronic regions (42.84%), with the remaining ones located downstream of genes (24.99%), upstream of genes (18.31%), in exonic regions (12.73%), and in splice sites (1.13%). Considering mutations in coding regions, 18,047 mutations (54.48%) were classified as missense, 14,875 (44.9%) were classified as synonymous and 204 (0.62%) were classified as nonsense. These genomic resources will be the prerequisite for genome-wide association studies (GWAS), with the ultimate aim of uncovering genes linked to traits of agronomic interest and environmental adaptation to be used in the genetic improvement of the fig tree.